class: center, middle, inverse, title-slide .title[ # World of Microbiome ] .author[ ###
Ragavi Shanmugam
• 28-Apr-2023 ] .institute[ ### Zifo RnD Solutions ] --- exclude: true count: false <link href="https://fonts.googleapis.com/css?family=Roboto|Source+Sans+Pro:300,400,600|Ubuntu+Mono&subset=latin-ext" rel="stylesheet"> <link rel="stylesheet" href="https://use.fontawesome.com/releases/v5.3.1/css/all.css" integrity="sha384-mzrmE5qonljUremFsqc01SB46JvROS7bZs3IO2EmfFsd15uHvIt+Y8vEf7N7fWAU" crossorigin="anonymous"> <!-- ------------ Only edit title, subtitle & author above this ------------ --> --- ## What is a Microbiome ? <br> <img src="data:image/png;base64,#data/microbiome/microbiome.jpg" width="100%" style="display: block; margin: auto;" /> --- ## What is Microbiome ? <br> * The microbiome is the community of microorganisms (such as fungi, bacteria and viruses) that exists in a particular environment (Types of Microbiome: 1. Soil Microbiome (Most complex) 2. Marine microbiome 3. Plant microbiome 4. Animal Microbiome (Ex. Chicken gut microbiome) 5. Human microbiome (Ex. Human gut microbiome) * In humans, the term is often used to describe the microorganisms that live in or on a particular part of the body, such as the skin or gastrointestinal tract. These groups of microorganisms are dynamic and change in response to a host of environmental factors, such as exercise, diet, medication and other exposures. * Microbiome research mostly looks at bacteria and fungi and rarely into archaea, viruses and other types. <img src="data:image/png;base64,#data/microbiome/microbiome2.jpg" width="50%" style="display: block; margin: auto;" /> --- ## Why study Microbiome ? <br> * We know the microbiome is important for maintaining human health, and when things go wrong it can contribute to disease. In order to understand how microbes, influence human disease, we first need to understand the microbial make up of a healthy person—what types of microbes are present, and what are they doing? <br> <img src="data:image/png;base64,#data/microbiome/gut_microbiome.jpg" width="70%" style="display: block; margin: auto;" /> --- ## What is bacteria ? .pull-left-40[ * Bacterial Genome: 1. Single chromosome 2. Mostly circular 3. Contains about 500-7500 genes 4. Genome size ranges from 400kbp – 13 million base pairs ] .pull-right-60[ <img src="data:image/png;base64,#data/microbiome/bac_cell.jpg" width="60%" style="display: block; margin: auto;" /> <br> <img src="data:image/png;base64,#data/microbiome/bac_genome.jpg" width="90%" style="display: block; margin: auto;" /> ] --- ## Prokaryote Ribose and 16S rRNA <br> <img src="data:image/png;base64,#data/microbiome/ribosome.jpg" width="100%" style="display: block; margin: auto;" /> --- ## 16S rRNA sequence <br> <img src="data:image/png;base64,#data/microbiome/16S.jpg" width="100%" style="display: block; margin: auto;" /> <br> The 16S rRNA gene is used for phylogenetic studies as it is highly conserved between different species of bacteria and archaea. Provides very good resolution till genus level and to some extent species level. There could be one or more copies of 16SrRNA in a bacterial genome. --- ## Comparison metagenomics VS. 16S rRNA <br> <img src="data:image/png;base64,#data/microbiome/comparison.jpg" width="100%" style="display: block; margin: auto;" /> --- ## Comparison metagenomics VS. 16S rRNA <br> <img src="data:image/png;base64,#data/microbiome/comparison2.jpg" width="100%" style="display: block; margin: auto;" /> --- ## 16s rRNA processing pipeline <br> <img src="data:image/png;base64,#data/microbiome/process_pipeline.jpg" width="100%" style="display: block; margin: auto;" /> --- ## Shotgun Metagenomics Pipeline <br> <img src="data:image/png;base64,#data/microbiome/shotgun.jpg" width="100%" style="display: block; margin: auto;" /> --- ## Suites of analysis tools <br> <img src="data:image/png;base64,#data/microbiome/tools.jpg" width="100%" style="display: block; margin: auto;" /> --- ## The taxonomic and functional compositions of a microbiome <br> <img src="data:image/png;base64,#data/microbiome/taxonomic.jpg" width="70%" style="display: block; margin: auto;" /> --- ## The taxonomic and functional compositions of a microbiome <br> <img src="data:image/png;base64,#data/microbiome/taxonomic2.jpg" width="100%" style="display: block; margin: auto;" /> --- ## Diversity estimates are a central topic in microbiome data analysis <br> ### Alpha, Beta and Gamma diversity <br> * The α-diversity is just the diversity of each site (local species pool). * The β-diversity represents the differences in species composition among sites. * The γ-diversity is the diversity of the entire landscape (regional species pool). * Shannon index α-diversity Test- Shannon index measures how evenly the microbes are distributed in a sample. It answers the question "How different?" How are the microbes balanced to each other? Do we have species evenness (similar abundance level) or do some species dominate others? ` --- ## Diversity estimates are a central topic in microbiome data analysis <br> <img src="data:image/png;base64,#data/microbiome/diversity.jpg" width="100%" style="display: block; margin: auto;" /> --- ## The developing gut microbiome and major influencing environmental factors <br> <img src="data:image/png;base64,#data/microbiome/diversity2.jpg" width="100%" style="display: block; margin: auto;" /> --- ## Bibliography <br> * [Tools for Analysis of the Microbiome](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7598837/) * [Best practices for analysing microbiomes](http://users.encs.concordia.ca/~gregb/home/PDF/best-practices-analysing-microbiomes-nat2018.pdf) <!-- --------------------- Do not edit this and below --------------------- --> --- name: end_slide class: end-slide, middle count: false # Thank you. Questions? .end-text[ <p class="smaller"> <span class="small" style="line-height: 1.2;">Graphics from </span><img src="./assets/freepik.jpg" style="max-height:20px; vertical-align:middle;"><br> Created: 28-Apr-2023 • James Ashmore • <a href="https://www.zifornd.com/category/omics-bioinformatics">Bioinformatics</a> • <a href="https://www.zifornd.com">Zifo</a> </p> ]